This markdown summarises the output from MRIQC (https://mriqc.readthedocs.io/en/latest/about.html), a tool developed by the Poldrack Lab at Stanford University. This software extracts IQMs (Image Quality Metrics). Of note, many of those IQMs are “no-reference” metrics. The software implements nipype workflows relying on FSL, ANTs and AFNI.

The workflow was specified as the following:
* threshold for frame wise displacement 0.5 (this is similar to what has been suggested by Powers et al., 2005). * head motion correction was performed using AFNI’s 3dvolreg * additonally, despiking and slice timing correction has been performed

I used the raw nifti files (as they came out of the scanner), but concatenated them so that the time series only includes volumes covering the task. This was necessary because we had to stop the scanner manually at the end of the task.

All images share the following scan paramters:

In total, there are the following output parameters:

Below, each of these parameters will be defined. Definitions have been copied from https://sarenseeley.github.io/BIDS-fmriprep-MRIQC.html#mriqc
Additionally, for each of these parameters, four graphs have been created to explore them in the sample:

  1. Histogram for all scans
  2. Histogram divided by group (control vs experimental) and task (magictricks vs rest)
  3. Boxplot for each acquisition (magictricks_run-1 vs. magictricks_run-2 vs. magictricks_run-3 vs. rest_run-1 vs. rest_run-2)
    In the boxplot, outliers are determined as: value < quantile(value, 0.25) - 1.5 * IQR(value) | value > quantile(value, 0.75) + 1.5 * IQR(value). If a value was an outlier, it was labeled using subject ID. The labels are printed in black if this subject belongs to the control group and in grey if the subject belongs to the experimental group.
  4. Spaghettiplot highlighting the timecourse of each of these parameters for each subject
    In the spaghetti plot, a subject was labeled if any of the values over time were larger than mean(value) + 1SD(value). Please note that the line for subject 16 makes a little dip for magictricks_run-2. This is because the scanner had to be stopped during the second block, so there are two acqusitions (both covering approximately half of the block).

Summary aor

Definition: AFNI’s outlier ratio. Mean fraction of outliers per fMRI volume, from AFNI’s 3dToutcount. Higher values indicate lower quality.

Interpretation: aor values are low and do not differ depending on task or group. Additionally, there seems to be some variation throughout the experiment.

Mean of subject-wise mean: 0.0027
SD of subject-wise mean: 0.0014
Mean of subject-wise SD: 0.0017
SD of subject-wise SD: 0.0014

Summary aqi

Definition: AFNI’s quality index. Mean quality index, from AFNI’s 3dTqual. Values close to 0 indicate higher quality.

Interpretation: aqi are low and comparable for both tasks and groups. There is some variability throughout the experiement.

Mean of subject-wise mean: 0.0052
SD of subject-wise mean: 0.0021
Mean of subject-wise SD: 0.0016
SD of subject-wise SD: 8e-04

Summary dummy_trs

Definition: Dummy scans. Number of volumes in the beginning of the fMRI timeseries identified as non-steady state.

Interpretation: Very low prevelence of dummy scans, max = 3.

Mean of subject-wise mean: 0.248
SD of subject-wise mean: 0.2573
Mean of subject-wise SD: 0.4011
SD of subject-wise SD: 0.3794

Summary dvars_nstd

Definition: Derivatives of variance. The average change in mean intensity between each pair of fMRI volumes in a series. Higher values indicate more dramatic changes (e.g., due to motion or spiking).

Interpretation: Raw derivatives of variance look comparible across groups and tasks, few outliers (e.g. sub-control037, sub-control045, sub-experimental016).

Mean of subject-wise mean: 30.1809
SD of subject-wise mean: 3.7044
Mean of subject-wise SD: 1.8208
SD of subject-wise SD: 1.6951

Summary dvars_std

Definition: Derivatives of variance. The average change in mean intensity between each pair of fMRI volumes in a series. Higher values indicate more dramatic changes (e.g., due to motion or spiking). The dvars_std metric is normalized with the standard deviation of the temporal difference time series.

Interpretation: Standardised derivatives of variance look similar across groups and tasks. These values are also stable across the course of the experiment.

Mean of subject-wise mean: 1.1098
SD of subject-wise mean: 0.053
Mean of subject-wise SD: 0.0455
SD of subject-wise SD: 0.0181

Summary dvars_vstd

Definition: Derivatives of variance. The average change in mean intensity between each pair of fMRI volumes in a series. Higher values indicate more dramatic changes (e.g., due to motion or spiking). The dvars_vstd is a voxel-wise standardization of DVARS, where the temporal difference time series is normalized across time by that voxel standard deviation across time, before computing the RMS of the temporal difference [Nichols2013].

Interpretation: Voxel-wise Standardized derivatives of variance are biased by one outlier (sub-control049_task-magictrickwatching_run-2), but otherwise low.

Mean of subject-wise mean: 16169.07
SD of subject-wise mean: 114321.4
Mean of subject-wise SD: 36152.71
SD of subject-wise SD: 255629.6

Summary efc

Definition: Entropy-focus criterion. Shannon entropy criterion. Higher values indicate more ghosting and/or head motion blurring.

Interpretation: No values above 0.55, groups and task look very similar, values constant throughout the duration of the experiment.

Mean of subject-wise mean: 0.4735
SD of subject-wise mean: 0.0285
Mean of subject-wise SD: 0.0028
SD of subject-wise SD: 0.0022

Summary fber

Definition: Foreground-background energy ratio. The variance of voxels inside the brain divided by the variance of voxels outside the brain. Higher values indicate higher quality.

Interpretation: Values comparable for both groups and tasks, only outlier with higher values (i.e. extremely good scans).

Mean of subject-wise mean: 5738985
SD of subject-wise mean: 5145258
Mean of subject-wise SD: 4136873
SD of subject-wise SD: 4632153

Summary fd_mean

Definition: Framewise displacement - mean. A measure of subject head motion, which compares the motion between the current and previous volumes.Higher values indicate lower quality.

Interpretation: Mean framewise displacement looks comparable across tasks and groups, though some subjects have high values (e.g. sub-control037, sub-control045, sub-experimental016). Interestingly, average relative movement seems to be fairly stable within each participant throughout the course of the experiment - in comparison to what I reported in previous mark downs.

Mean of subject-wise mean: 0.1324
SD of subject-wise mean: 0.0513
Mean of subject-wise SD: 0.0258
SD of subject-wise SD: 0.0257

Summary fd_num

Definition: Framewise displacement - number. Number of timepoints with framewise displacement >0.5mm. Higher values indicate lower quality.

Interpretation: Number of scans above 0.5mm threshold is fairly low and comparable between tasks and groups. There are outliers, especially sub-control037, sub-control045. Again, values are fairly constant over the course of the experiment.

Mean of subject-wise mean: 5.6187
SD of subject-wise mean: 11.4456
Mean of subject-wise SD: 4.4223
SD of subject-wise SD: 8.5533

Summary fd_perc

Definition: Framewise displacement - percent. Percent of timepoints with framewise displacement >0.5mm. Higher values indicate lower quality.

Interpretation: Percentage of scans above threshold of 0.5mm is low on average, but also biased by outliers.

Mean of subject-wise mean: 1.6263
SD of subject-wise mean: 3.2786
Mean of subject-wise SD: 1.2807
SD of subject-wise SD: 2.469

Summary fwhm_avg

Definition: Full-width half-maximum smoothness. Image blurriness (full-width half-maximum) - average. Higher values indicate a blurrier image.

Interpretation: Average smoothness is comparable across tasks and groups, and has a small range [2.5; 2.9] and is stable throught the experiment.

Mean of subject-wise mean: 2.6544
SD of subject-wise mean: 0.0743
Mean of subject-wise SD: 0.0239
SD of subject-wise SD: 0.0115

Summary fwhm_x

Definition: Full-width half-maximum smoothness. Image blurriness (full-width half-maximum) - x axis Higher values indicate a blurrier image.

Interpretation: Smoothness on x axis is comparable across tasks and groups, and has a small range [2.4; 2.9] and is stable throught the experiment.

Mean of subject-wise mean: 2.6208
SD of subject-wise mean: 0.0939
Mean of subject-wise SD: 0.0267
SD of subject-wise SD: 0.0153

Summary fwhm_y

Definition: Full-width half-maximum smoothness. Image blurriness (full-width half-maximum) - y axis Higher values indicate a blurrier image.

Interpretation: Smoothness on y axis is comparable across tasks and groups, and has a small range [2.7; 3.3] and is stable throught the experiment.

Mean of subject-wise mean: 3.0181
SD of subject-wise mean: 0.1128
Mean of subject-wise SD: 0.0349
SD of subject-wise SD: 0.0203

Summary fwhm_z

Definition: Full-width half-maximum smoothness. Image blurriness (full-width half-maximum) - z axis Higher values indicate a blurrier image.

Interpretation: Smoothness on z axis is comparable across tasks and groups, and has a small range [2.1;2.8] and is stable throught the experiment.

Mean of subject-wise mean: 2.3244
SD of subject-wise mean: 0.0818
Mean of subject-wise SD: 0.0292
SD of subject-wise SD: 0.0301

Summary gcor

Definition: Global correlation. Average correlation of all pairs of voxel time series inside of the brain. Illustrates differences between data due to motion/physiological noise/imaging artifacts. Values closer to zero are better.

Interpretation: Global correlation is small and does not differ betweem groups and tasks. Values also seem moderately stable, but also show variations throughout the course of the experiment.

Mean of subject-wise mean: 0.0175
SD of subject-wise mean: 0.0071
Mean of subject-wise SD: 0.0056
SD of subject-wise SD: 0.0029

Summary gsr_x

Definition: Ghost-to-signal ratio. Ghost-to-signal ratio along the x encoding axis. Higher values indicate lower quality.

Interpretation: Low GSR values in x axis for both groups and tasks, values stable.

Mean of subject-wise mean: 0.0312
SD of subject-wise mean: 0.02
Mean of subject-wise SD: 0.0023
SD of subject-wise SD: 0.0023

Summary gsr_y

Definition: Ghost-to-signal ratio. Ghost-to-signal ratio along the y encoding axis. Higher values indicate lower quality.

Interpretation: Low GSR values in y axis for both groups and tasks, values stable, but sub-control007 and sub-control031 are identified as outliers.

Mean of subject-wise mean: 0.0293
SD of subject-wise mean: 0.0144
Mean of subject-wise SD: 0.0021
SD of subject-wise SD: 0.0015

Summary size_t

Definition: Number of volumes minus dummy TRs.

Interpretation: size_t looks as expected given that there is some variation in the length of task runs.

Mean of subject-wise mean: 347.808
SD of subject-wise mean: 8.2685
Mean of subject-wise SD: 46.8546
SD of subject-wise SD: 5.4911

Summary snr

Definition: Signal-to-noise ratio. Signal-to-noise ratio within the tissue mask. Higher values indicate higher quality.

Interpretation: snr looks comparable between groups and tasks and stable throughout the experiment. Sub-experimental014 has outlying low values.

Mean of subject-wise mean: 2.0186
SD of subject-wise mean: 0.1763
Mean of subject-wise SD: 0.0318
SD of subject-wise SD: 0.0301

Summary tsnr

Definition: Temporal signal-to-noise ratio. Temporal signal-to-noise ratio taking into account mean signal over time. Higher values indicate higher quality.

Interpretation: tsnr is similar between groups and tasks, no outliers in either direction, but values show variance throughout the experiment.

Mean of subject-wise mean: 42.9263
SD of subject-wise mean: 7.2881
Mean of subject-wise SD: 6.2081
SD of subject-wise SD: 2.6197

Summary summary_bg_k

Definition: Summary statistics for average intensities in background: kurtosis

Interpretation: Some outliers in BG kurtosis, but values are stable and comparible groups and tasks.

Mean of subject-wise mean: 58.3665
SD of subject-wise mean: 30.7407
Mean of subject-wise SD: 4.5326
SD of subject-wise SD: 4.0237

Summary summary_bg_mad

Definition: Summary statistics for average intensities in background: median absolute deviation (MAD)

Interpretation: Some outliers in BG MAD, but values are stable and comparible groups and tasks.

Mean of subject-wise mean: 0.3353
SD of subject-wise mean: 0.1883
Mean of subject-wise SD: 0.1082
SD of subject-wise SD: 0.0736

Summary summary_bg_mean

Definition: Summary statistics for average intensities in background: mean

Interpretation: Stable BG mean values.

Mean of subject-wise mean: 10.99
SD of subject-wise mean: 4.1651
Mean of subject-wise SD: 0.5807
SD of subject-wise SD: 0.9188

Summary summary_bg_median

Definition: Summary statistics for average intensities in background: median

Interpretation: Stable BG median values.

Mean of subject-wise mean: 0.2322
SD of subject-wise mean: 0.1322
Mean of subject-wise SD: 0.0759
SD of subject-wise SD: 0.0528

Summary summary_bg_n

Definition: Summary statistics for average intensities in background: n (number of voxels)

Interpretation: Stable number of BG voxels across tasks (as expected). Low values for sub-experimental014, but that’s due to large head.

Mean of subject-wise mean: 79196.34
SD of subject-wise mean: 5578.273
Mean of subject-wise SD: 324.8696
SD of subject-wise SD: 538.2043

Summary summary_bg_p05

Definition: Summary statistics for average intensities in background: 5% percentile

Interpretation: BG 5% percentaile similar across groups and tasks, but some outliers and variation across the tasks.

Mean of subject-wise mean: 0.0021
SD of subject-wise mean: 0.0024
Mean of subject-wise SD: 0.0017
SD of subject-wise SD: 0.0017

Summary summary_bg_p95

Definition: Summary statistics for average intensities in background: 95% percentile

Interpretation: BG 95% percentaile more stable across the experiment and similar across groups and tasks.

Mean of subject-wise mean: 69.6583
SD of subject-wise mean: 28.1033
Mean of subject-wise SD: 4.0083
SD of subject-wise SD: 7.1157

Summary summary_bg_stdv

Definition: Summary statistics for average intensities in background: standard deviation

Interpretation: BG STD comparable across groups and tasks. So reason to assume any slice or voxel outages.

Mean of subject-wise mean: 39.5643
SD of subject-wise mean: 12.8173
Mean of subject-wise SD: 1.4152
SD of subject-wise SD: 1.8978

Summary summary_fg_k

Definition: Summary statistics for average intensities in foreground: kurtosis

Interpretation: Some outliers in FG kurtosis, but values are stable and comparible groups and tasks.

Mean of subject-wise mean: 0.5517
SD of subject-wise mean: 0.5618
Mean of subject-wise SD: 0.0995
SD of subject-wise SD: 0.1273

Summary summary_fg_mad

Definition: Summary statistics for average intensities in foreground: median absolute deviation (MAD)

Interpretation: No outliers in FG MAD, but values are stable and comparible groups and tasks.

Mean of subject-wise mean: 199.2405
SD of subject-wise mean: 31.9518
Mean of subject-wise SD: 5.8489
SD of subject-wise SD: 3.9886

Summary summary_fg_mean

Definition: Summary statistics for average intensities in foreground: mean

Interpretation: Stable FG mean values.

Mean of subject-wise mean: 449.2453
SD of subject-wise mean: 42.1464
Mean of subject-wise SD: 6.8991
SD of subject-wise SD: 4.8276

Summary summary_fg_median

Definition: Summary statistics for average intensities in foreground: median

Interpretation: Stable FG median values.

Mean of subject-wise mean: 411.6038
SD of subject-wise mean: 35.8233
Mean of subject-wise SD: 6.0196
SD of subject-wise SD: 4.2644

Summary summary_fg_n

Definition: Summary statistics for average intensities in foreground: n (number of voxels)

Interpretation: Stable number of FG voxels across tasks (as expected). High values for sub-experimental014, but that’s due to large head.

Mean of subject-wise mean: 37901.74
SD of subject-wise mean: 4728.203
Mean of subject-wise SD: 196.1244
SD of subject-wise SD: 302.0331

Summary summary_fg_p05

Definition: Summary statistics for average intensities in foreground: 5% percentile

Interpretation: FG 5% percentile similar across groups, tasks, and the course of the experiment.

Mean of subject-wise mean: 182.2307
SD of subject-wise mean: 12.4931
Mean of subject-wise SD: 1.997
SD of subject-wise SD: 1.0539

Summary summary_fg_p95

Definition: Summary statistics for average intensities in foreground: 95% percentile

Interpretation: FG 95% percentile more stable across the experiment and similar across groups and tasks.

Mean of subject-wise mean: 839.7946
SD of subject-wise mean: 100.784
Mean of subject-wise SD: 16.7174
SD of subject-wise SD: 12.3028

Summary summary_fg_stdv

Definition: Summary statistics for average intensities in foreground: standard deviation

Interpretation: BG STD comparable across groups and tasks. So reason to assume any slice or voxel outages.

Mean of subject-wise mean: 206.279
SD of subject-wise mean: 31.2745
Mean of subject-wise SD: 5.5079
SD of subject-wise SD: 3.9783